Bio::Phylo::NeXML::DOM::Document - XML DOM Abstract class for flexible document object model implementation
Not used directly.
This module describes an abstract implementation of a DOM document as expected by Bio::Phylo. The methods here must be overridden in any concrete implementation. The idea is that different implementations use a particular XML DOM package, binding the methods here to analogous package methods.
This set of methods is intentionally minimal. The concrete instances of this class should inherit both from DocumentI and the underlying XML DOM object class, so that package-specific methods can be directly accessed from the instantiated object.
Mark A. Jensen - maj -at- fortinbras -dot- us
Type : Constructor Title : new Usage : $doc = Bio::Phylo::NeXML::DOM::Document->new(@args) Function: Create a Document object using the underlying package Returns : Document object or undef on fail Args : Package-specific arguments
Type : Factory method Title : parse_document Usage : $doc = $dom->parse_document($text) Function: Create a new XML DOM document from XML text Returns : DOM document Args : An XML String
Type : Mutator Title : set_encoding Usage : $doc->set_encoding($enc) Function: Set encoding for document Returns : True on success Args : Encoding descriptor as string
Type : Accessor Title : get_encoding Usage : $doc->get_encoding() Function: Get encoding for document Returns : Encoding descriptor as string Args : none
Type : Mutator Title : set_root Usage : $doc->set_root($elt) Function: Set the document's root element Returns : True on success Args : Element object
Type : Accessor Title : get_root Usage : $doc->get_root() Function: Get the document's root element Returns : Element object or undef if DNE Args : none
Type : Accessor Title : get_element_by_id Usage : $doc->get_element_by_id($id) Function: Get element having id $id Returns : Element object or undef if DNE Args : id designator as string
Type : Accessor Title : get_elements_by_tagname Usage : $elt->get_elements_by_tagname($tagname) Function: Get array of elements having given tag name Returns : Array of elements or undef if no match Args : tag name as string
Type : Serializer Title : to_xml Usage : $doc->to_xml Function: Create XML string from document Returns : XML string Args : Formatting arguments as allowed by underlying package
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.